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However all of them were inactive (i.e. just passive virulent files that weren't configured by the system to be loaded anywhere). Curiously enough, it flagged a JPEG file as a virus. I inspected it with a binary editor and apparently it was a renamed zip file containing an EXE. It came attached with some email.

The thing is, you now know the system was infected but you don't really know it isn't still compromised by something the anti-virus tool didn't spot. So you've lost the best part of a day scanning a system and you can still only be sure it's clean by reinstalling everything. Not unsurprised to see executables hidden inside renamed files though, that's pretty common.